The pipe organ was once the most sophisticated instrument ever built, filling cathedrals with music to "elevate the soul". But it somehow got stuck in the cinemas and churches of middle America, a symbol of deference and decay. Cameron Carpenter, the instrument's punk prodigy, is scathing about those responsible for its fate. "The supreme indifference of organists to the needs and wishes of a broader audience can be observed at an organ concert in any city," he declaims. "The audience will be comprised of either organists, or inveterate organ nerds who carry their clothes around in paper bags and breathe through their mouths."

Carpenter's strategy for wrenching the instrument out of its torpor is first to dress like an ice-dancing Skrillex, then to deliver performances of great physical drama, his body convulsing, his legs moving like Fred Astaire. This would be mere window dressing, however, were his performances not both cerebral and emotional explorations of an unexpected repertoire. "If music is a language and the organ is a megaphone, then the message is really what it comes down to," he says. "It has something to do with ecstasy. In fact, one of the things that first attracted me to the organ was its violence. There can be a great beauty to expressive violence, and the organ has it in vast amounts. In the Bach cantata we're going to do at Manchester, you feel that you may have brushed up against something very evil indeed, and come out of it duly reminded of how glad you are to be alive."

He'll perform Bach's Ich Will Den Kreuzstab Gerne Tragen alongside Shostakovich's Suite On Verses Of Michelangelo Buonarroti, in cahoots with two fellow creative iconoclasts: director Peter Sellars and bass baritone Eric Owens. Carpenter, who is only 31, describes Sellars as "a mentor, and a person who has consistently been at the forefront of the idea that not only classical music, but also dance and drama, should be examined anew." Owens, he says, is "an organ of a man – a giant temple of tone. I'm trying to frame him in a way that is going to be equal to the art inside the frame."

Carpenter says he'll relish "not having to be Atlas on stage, not having to hold the entire performance on my shoulders," as he has done throughout his career on what he calls "the loneliest instrument." He began playing after "as a tiny child I saw a highly evocative encyclopedia entry on an organist playing in a movie palace. It was almost sinister in its power, and I was forever ruined to serious dedication to any other instrument." An education at the Juilliard conservatory in New York led to a recording contract and the first ever Grammy nomination for a solo organist, then on to a globetrotting series of tradition-baiting performances.

For Carpenter, it's not just the harrumphing of the organ nerds that raises his hackles – it's the church that so many organs are stationed in. "For centuries, the organists themselves have been stamped out – go into to a big English church and see if you can see the person playing. This kind of vile pissing down upon the person who is actually completely responsible for the music, for me, has parallels with the many ways in which science and the arts are thanklessly pressed into the service of religion. Like many other secular aspects of art, the organ has over the centuries been co-opted into being a handmaiden for old men who would lie to children." He scoffs, wonderfully, at the "cliched hobgoblinry of ecclesiastica", although ultimately he asserts that "my values are artistic, not religio-political".

As a result of his distaste for the pipe organ's traditional home, he's currently trying to democratise the instrument by building his own portable, digital version that he'll tour with from 2014. "What I'm attempting to bring to the organ is modernity and globalisation, because I want to play the world's greatest organ in Tokyo and at the Royal Albert Hall. I am very lucky to live in the first time where technologically I have the ability to do that – at risk of controversy and to my reputation. But, as Jean Cocteau said, reputation is the smallest part of me."